+Open data
-Basic information
Entry | Database: PDB / ID: 1yfo | ||||||
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Title | RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA, DOMAIN 1 FROM MOUSE | ||||||
Components | RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA | ||||||
Keywords | HYDROLASE / SIGNAL TRANSDUCTION / RECEPTOR / GLYCOPROTEIN / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / positive regulation of oligodendrocyte differentiation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / synaptic membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse ...NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / positive regulation of oligodendrocyte differentiation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / synaptic membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway / receptor complex / focal adhesion / protein-containing complex binding / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Bilwes, A.M. / Noel, J.P. | ||||||
Citation | Journal: Nature / Year: 1996 Title: Structural basis for inhibition of receptor protein-tyrosine phosphatase-alpha by dimerization. Authors: Bilwes, A.M. / den Hertog, J. / Hunter, T. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfo.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfo.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yfo_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 1yfo_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 1yfo_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1yfo_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfo ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfo | HTTPS FTP |
-Related structure data
Related structure data | 2hnpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999983, 0.001238, -0.005715), Vector: |
-Components
#1: Protein | Mass: 34894.770 Da / Num. of mol.: 2 / Fragment: MEMBRANE PROXIMAL CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: TYPE I MEMBRANE PROTEIN / Cell line: BL21 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P18052, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | Compound details | RESIDUES 379 - 386 WERE NOT MODELLED FOR EACH MONOMER TRYPSIN CUT AT 385 OR 386. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 44 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 8000 0.3 M AMMONIUM ACETATE, 50 MM SODIUM ACETATE PH 5, 2 MM DTT. ETHYLENE GLYCOL 20% WAS USED AS A CRYOPROTECTANT., pH 5.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 14, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→23 Å / Num. obs: 22317 / % possible obs: 82.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.046 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 1 % / Mean I/σ(I) obs: 7 / Rsym value: 0.104 / % possible all: 17.4 |
Reflection | *PLUS Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 17.4 % / Rmerge(I) obs: 0.104 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HNP Resolution: 2.25→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.281 |